Full Record - Taxonomic identification and molecular barcoding of sea cucumbers collected from Rothera Research Station, Antarctic Peninsula, Antarctica, in 2012 and 2021

Taxonomic identification and molecular barcoding of sea cucumbers collected from Rothera Research Station, Antarctic Peninsula, Antarctica, in 2012 and 2021

GB/NERC/BAS/PDC/01754

Abstract:
This dataset describes the taxonomic identification and molecular barcoding of the five species of sea cucumber (three common and two very rare species) identified from diver-collected samples in Ryder Bay near Rothera Research Station, Antarctic Peninsula, Antarctica, in 2012 and 2021. Specimens of each species were registered and taxonomic identification performed at the Museums Victoria, Melbourne, Australia with additional molecular barcoding performed using the cytochrome c oxidase sub unit 1 (CO1) gene at the British Antarctic Survey.

This study was funded by core funding to UKRI NERC-BAS.

Citation:
Clark, M.S., Mackenzie, M., & Frontier, N. (2023). Taxonomic identification and molecular barcoding of sea cucumbers collected from Rothera Research Station, Antarctic Peninsula, Antarctica, in 2012 and 2021 (Version 1.0) [Data set]. NERC EDS UK Polar Data Centre. https://doi.org/10.5285/dc016e6a-1b1e-4fcf-aed0-c6b2236f849a

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https://ramadda.data.bas.ac.uk/repository/entry/show?entryid=dc016e6a-1b1e-4fcf-aed0-c6b2236f849a

RELATED DATA SET DESCRIPTION

License

Access:	None.
Use:	Data released under Open Government Licence V3.0: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/.

Authors

Name	UK Polar Data Centre
Role(s)	Metadata Author
Organisation	British Antarctic Survey

Name	Prof Melody S Clark
Role(s)	Investigator
Organisation	British Antarctic Survey

Name	Ms Melanie Mackenzie
Role(s)	Investigator
Organisation	Museums Victoria

Name	Ms Nadia Frontier
Role(s)	Investigator
Organisation	British Antarctic Survey

Basic Information

Creation Date:	2023-06-29
Dataset Progress:	Complete
Dataset Language:	English
ISO Topic Categories:	Biota Environment Oceans
Parameters:	Biosphere > Animal Taxonomy > Echinoderms Oceans > Marine Environment Monitoring

Additional Information

Reference:	Five species of sea cucumber were hand-collected by SCUBA divers from Ryder Bay near Rothera Research Station, Adelaide Island, Antarctic Peninsula (67.56861 S, 68.125 W) during two austral summers (2012 and 2021) at depths of 10-15m. A whole animal from each species was preserved in 96% ethanol for taxonomic identification. Tentacles from further specimens were also preserved in 96% ethanol for molecular barcoding. Taxonomic identification was performed at the Melbourne Museum, Victoria, Australia (Figure 1; Table 1). Molecular barcoding was performed at the British Antarctic Survey using the following protocol: DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen, UK) following manufacturer's instructions. DNA samples were amplified using the primers COIef (5'-ATAATGATAGGAGG[A/G]TTTGG-3') and COIer (5'-GCTCGTGT[A/G]TCTAC[A/G]TCCAT-3'). It was not possible to successfully amplify the Heterocucumis sp. and therefore to overcome this problem species-specific primers, COI_Het_F1 (5'-ATTACTCCCTCCTTCATTA-3') and COI_Het_R1 (5'-GGCTCTTTCTTTCCTCTAT-3'), were designed using the Primer3 program by Michelle King and Elaine Fitzcharles at the British Antarctic Survey. The PCR reactions were carried out on an Alpha Cycler (PCR max) using 2x MyTaq HS Red Mix (Meridian) according to manufacturer's instructions with the following reaction conditions: 94°C for 5 minutes, then 35 cycles of 94°C for 45 Seconds, 50°C for 45 Seconds, 72°C for 1 minute, and a final step of 72°C for 10 minutes. The PCR products were sent to Source Bioscience (Cambridge, UK) for Sanger sequencing in both forward and reverse directions. The sequences were of each species were assembled and edited using Geneious Prime Version 2022.2.2 to remove primer sequences. Initial collections of sea cucumbers for taxonomic identification (Heterocucumis steineni, Cucumaria georgiana, Echinopsolus charcoti) were made in 2012 under Antarctic collection permit number S7-05/2012 granted under Section 7 of the Antarctic Act 1994. Further collections for all five species were made in 2021 under Antarctic collection permit no BAS-S7-2021/01 granted under Section 7 of the Antarctic Act 1994 for the taxonomic identification of Cucamba psolidiformis and Staurocucumis liouvillei and molecular barcoding of all five species. Taxonomic evaluation identified the five holothuroids as the following species: Heterocucumis steineni (Ludwig 1898) Figure 1 A & B), Cucumaria georgiana (Lampert, 1886) [as Cucumaria attenuata Vaney 1906] (Figure 1 C & D), Echinopsolus charcoti (Figure 1 E & F), Cucamba psolidiformis (Figure 1 G & H) and Staurocucumis liouvillei (Figure 1 I & J). A 634bp CO1 sequence was obtained for Cucumaria georgiana, Echinopsolus charcoti, Cucamba psolidiformis and Staurocucumis liouvillei, whilst a shorter 435bp CO1 fragment was obtained for Heterocucumis steineni. These sequences were submitted to NCBI Bank-IT with accession numbers OR150695-OR150699 (Table 1).

Reference:

Five species of sea cucumber were hand-collected by SCUBA divers from Ryder Bay near Rothera Research Station, Adelaide Island, Antarctic Peninsula (67.56861 S, 68.125 W) during two austral summers (2012 and 2021) at depths of 10-15m. A whole animal from each species was preserved in 96% ethanol for taxonomic identification. Tentacles from further specimens were also preserved in 96% ethanol for molecular barcoding.

Taxonomic identification was performed at the Melbourne Museum, Victoria, Australia (Figure 1; Table 1). Molecular barcoding was performed at the British Antarctic Survey using the following protocol: DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen, UK) following manufacturer's instructions. DNA samples were amplified using the primers COIef (5'-ATAATGATAGGAGG[A/G]TTTGG-3') and COIer (5'-GCTCGTGT[A/G]TCTAC[A/G]TCCAT-3'). It was not possible to successfully amplify the Heterocucumis sp. and therefore to overcome this problem species-specific primers, COI_Het_F1 (5'-ATTACTCCCTCCTTCATTA-3') and COI_Het_R1 (5'-GGCTCTTTCTTTCCTCTAT-3'), were designed using the Primer3 program by Michelle King and Elaine Fitzcharles at the British Antarctic Survey. The PCR reactions were carried out on an Alpha Cycler (PCR max) using 2x MyTaq HS Red Mix (Meridian) according to manufacturer's instructions with the following reaction conditions: 94°C for 5 minutes, then 35 cycles of 94°C for 45 Seconds, 50°C for 45 Seconds, 72°C for 1 minute, and a final step of 72°C for 10 minutes. The PCR products were sent to Source Bioscience (Cambridge, UK) for Sanger sequencing in both forward and reverse directions. The sequences were of each species were assembled and edited using Geneious Prime Version 2022.2.2 to remove primer sequences.

Initial collections of sea cucumbers for taxonomic identification (Heterocucumis steineni, Cucumaria georgiana, Echinopsolus charcoti) were made in 2012 under Antarctic collection permit number S7-05/2012 granted under Section 7 of the Antarctic Act 1994. Further collections for all five species were made in 2021 under Antarctic collection permit no BAS-S7-2021/01 granted under Section 7 of the Antarctic Act 1994 for the taxonomic identification of Cucamba psolidiformis and Staurocucumis liouvillei and molecular barcoding of all five species.

Taxonomic evaluation identified the five holothuroids as the following species: Heterocucumis steineni (Ludwig 1898) Figure 1 A & B), Cucumaria georgiana (Lampert, 1886) [as Cucumaria attenuata Vaney 1906] (Figure 1 C & D), Echinopsolus charcoti (Figure 1 E & F), Cucamba psolidiformis (Figure 1 G & H) and Staurocucumis liouvillei (Figure 1 I & J). A 634bp CO1 sequence was obtained for Cucumaria georgiana, Echinopsolus charcoti, Cucamba psolidiformis and Staurocucumis liouvillei, whilst a shorter 435bp CO1 fragment was obtained for Heterocucumis steineni. These sequences were submitted to NCBI Bank-IT with accession numbers OR150695-OR150699 (Table 1).

Extent

Temporal Coverage:
Start Date	2021-01-01
End Date	2021-12-31

Start Date	2012-01-01
End Date	2012-12-31

Spatial Coverage:
Latitude
Southernmost	-67.56861
Northernmost	-67.56861
Longitude
Westernmost	-68.125
Easternmost	-68.125
Altitude
Min Altitude	N/A
Max Altitude	N/A
Depth
Min Depth	N/A
Max Depth	N/A

Location:
Location	Antarctica
Detailed Location	Antarctic Peninsula, Ryder Bay near Rothera Research Station

Storage

Data Storage:	Panel of pictures of each cucumber after taxonomic identification alongside photographs of living animals (Figure 1, pdf format). Table of all data associated with collections (Table1.pdf).